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[Seg3D] Re: Large Dataset on Windows 8


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  • From: anastasios.marmaras@uzh.ch
  • To: seg3d@sci.utah.edu
  • Subject: [Seg3D] Re: Large Dataset on Windows 8
  • Date: Thu, 18 Jul 2013 14:54:58 +0200
  • Importance: Normal
Hello Ayla,

Thank you very much for your response and the clarification regarding out-of-core data.

Unfortunately the log file contains nothing: When i make a new project, a long list of entries appear in the log. The last line of which is:

[2013-Jul-18 14:32:18|ActionNewProject.cc|145] SUCCESS: Successfully created new project 'Kidney21'.

(Kidney21 being the name of the project file.).

When i subsequently try to load the data stack (which takes a few minutes and crashes at 6.5 GB memory utilisation) the crash is silent, nothing new is written to the log file.

I am in general very willing to try out your test code. But would that involve recompiling Seg3D for windows ? If that's the case we will probably not have much luck with it because we do not have Visual Studio, or much experience with it here. (and we also do not have a linux machine with that amount of ram). If it is a matter of replacing some pre-compiled component i can go ahead with it.

Thanks again for your helpful response.

best regards,
Anastasios






-----Ayla Khan <ayla@sci.utah.edu> wrote: -----
To: seg3d@sci.utah.edu
From: Ayla Khan <ayla@sci.utah.edu>
Date: 07/17/2013 01:25AM
Subject: [Seg3D] Re: Large Dataset on Windows 8

Hi Anastasios,

Thank you for your feedback! Seg3D wraps ITK file importers, which have support for streaming very large datasets - the example cited is about 13GB. For TIFF stacks (and other file series types), this feature is on by default. Unfortunately, we don't have streaming support for the ITK filters implemented. If you're still willing to try to load your data, I'll send you ITK test code which only tries to load an image stack to see if that fails too.

Also, can you look in your user Seg3D AppData folder for log files corresponding to Seg3D sessions that crashed (the log file pattern is Seg3D_2.1.4_YYYYMMDDT1HHMM...)? Usually this is set up as AppData/Local/Seg3D2 under your user folder, but can also be found using the %appdata% environment variable.

Seg3D does not support virtual, or out-of-core data yet - it's a feature we are starting to research however. ImageVis3D is the only CIBC software product that supports this.

Ayla

On Jul 16, 2013, at 2:23 AM, anastasios.marmaras@uzh.ch wrote:

Hello,

I would like to start by saying that i recently found out about all the work you have been doing and have to say that i am very impressed. ImageVis3D and Seg3D are both great programs.

Onto what seems to be a bug report:

I have tried to load a 66 GB dataset onto Seg3D (v2.1.4). This was on a Windows 8 system with 256 GB of ram. To be more precise i tried to import a a stack of tiffs as a single layer data volume. The import process crashed. As a matter of fact it always crashes as soon as the memory used by Seg3D reaches about 6.5 GB. Could it be that there is some incompatibility with Windows 8 that causes that ? In any case i just wanted to report the behavior. Also, i would be very happy to investigate further if you would like me to.

On a similar note, i would also like to ask whether Seg3D already supports (or there is plan to support) working with virtual volumes, i.e. volumes too large to fit in memory which will instead be directly worked on the hard drive. (terribly slow, but in certain cases unavoidable). Just wondering whether something like that is supported or planned for Seg3D.

best regards,
Anastasios

--

University of Zurich
Dr. Anastasios Marmaras
Institute of Physiology
Interface Group
Y23 J 78
Winterthurerstrasse 190
CH-8057 Zurich
Tel. +41 44 635 50 56
anastasios.marmaras@uzh.ch

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